Variant X-20010875-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000379643.10(MAP7D2):c.2250C>T(p.Asp750Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,208,963 control chromosomes in the GnomAD database, including 67 homozygotes. There are 4,133 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0074 ( 2 hom., 214 hem., cov: 23)

Exomes 𝑓: 0.011 ( 65 hom. 3919 hem. )

Consequence

MAP7D2
ENST00000379643.10 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.08

Variant links:

Genes affected

MAP7D2 (HGNC:25899): (MAP7 domain containing 2) Predicted to be involved in microtubule cytoskeleton organization. Predicted to be active in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

MAP7D2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant X-20010875-G-A is Benign according to our data. Variant chrX-20010875-G-A is described in ClinVar as [Benign]. Clinvar id is 778201.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-20010875-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=1.08 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP7D2	NM_001168465.2 linkuse as main transcript	c.2250C>T	p.Asp750Asp	synonymous_variant	16/17	ENST00000379643.10	NP_001161937.1	Q96T17-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MAP7D2	ENST00000379643.10 linkuse as main transcript	c.2250C>T	p.Asp750Asp	synonymous_variant	16/17	1	NM_001168465.2	ENSP00000368964.5	Q96T17-2
MAP7D2	ENST00000379651.7 linkuse as main transcript	c.2127C>T	p.Asp709Asp	synonymous_variant	15/16	1		ENSP00000368972.3	Q96T17-1
MAP7D2	ENST00000443379.7 linkuse as main transcript	c.1992C>T	p.Asp664Asp	synonymous_variant	14/15	2		ENSP00000388239.3	Q96T17-4
MAP7D2	ENST00000452324.3 linkuse as main transcript	c.1971C>T	p.Asp657Asp	synonymous_variant	15/16	2		ENSP00000413301.3	Q96T17-5

Frequencies

GnomAD3 genomes

AF:

0.00738

AC:

824

AN:

111724

Hom.:

Cov.:

AF XY:

0.00631

AC XY:

214

AN XY:

33904

show subpopulations

Gnomad AFR

AF:

0.00179

Gnomad AMI

AF:

0.0103

Gnomad AMR

AF:

0.00181

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00149

Gnomad FIN

AF:

0.0113

Gnomad MID

AF:

0.00418

Gnomad NFE

AF:

0.0119

Gnomad OTH

AF:

0.00402

GnomAD3 exomes

AF:

0.00754

AC:

1383

AN:

183458

Hom.:

AF XY:

0.00736

AC XY:

500

AN XY:

67896

show subpopulations

Gnomad AFR exome

AF:

0.000988

Gnomad AMR exome

AF:

0.00124

Gnomad ASJ exome

AF:

0.0114

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00147

Gnomad FIN exome

AF:

0.0124

Gnomad NFE exome

AF:

0.0122

Gnomad OTH exome

AF:

0.00574

GnomAD4 exome

AF:

0.0112

AC:

12328

AN:

1097185

Hom.:

Cov.:

AF XY:

0.0108

AC XY:

3919

AN XY:

362721

show subpopulations

Gnomad4 AFR exome

AF:

0.00144

Gnomad4 AMR exome

AF:

0.00119

Gnomad4 ASJ exome

AF:

0.0122

Gnomad4 EAS exome

AF:

0.0000331

Gnomad4 SAS exome

AF:

0.00113

Gnomad4 FIN exome

AF:

0.0127

Gnomad4 NFE exome

AF:

0.0131

Gnomad4 OTH exome

AF:

0.00958

GnomAD4 genome

AF:

0.00737

AC:

824

AN:

111778

Hom.:

Cov.:

AF XY:

0.00630

AC XY:

214

AN XY:

33968

show subpopulations

Gnomad4 AFR

AF:

0.00178

Gnomad4 AMR

AF:

0.00181

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00150

Gnomad4 FIN

AF:

0.0113

Gnomad4 NFE

AF:

0.0119

Gnomad4 OTH

AF:

0.00397

Alfa

AF:

0.00906

Hom.:

Bravo

AF:

0.00626

EpiCase

AF:

0.0103

EpiControl

AF:

0.0101

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

5.9

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over